Re: [scipion-users] Combining 2 dataset --- coordinates/extraction issue

[Juha H. <juh...@he...>]

Dear All,

I am having the same issue.  I have data collected in two different
sessions and they have been exported from two different raw data folders.
When I combine two SetOfParticels using 'scipion - join sets' and try to
run 'relion - 3D auto-refine' I get the following error:

00029:     File
"/projappl/project_2001566/apps/scipion/2.0/software/lib/python2.7/site-packages/relion/convert/convert.py",
line 757, in convertBinaryFiles
00030:       pw.utils.createLink(rootDir, outputRoot)
00031:     File
"/projappl/project_2001566/apps/scipion/2.0/pyworkflow/utils/path.py", line
250, in createLink
00032:       relsource = join(relpath(sourcedir, destdir), basename(source))
00033:     File
"/projappl/project_2001566/apps/scipion/2.0/software/lib/python2.7/posixpath.py",
line 428, in relpath
00034:       raise ValueError("no path specified")
00035:   ValueError: no path specified
00036:   Protocol failed: no path specified
00037:   FAILED: convertInputStep, step 1

Best wishes,
Juha

On Thu, Nov 7, 2019 at 6:07 PM Dmitry Semchonok <Sem...@gm...> wrote:

> Dear colleagues,
>
>  I have 2 sets of particles from different micrographs that have the same
> pixel size.
>
>
>
> I want to join (combine) them and run all together.
>
>  What can be the strategy to do that?
>
>
>
>
> What I did
>
> a)     Combined 2 sets of micrographs (with which I worked
> independently).
>
> Combined 2 sets of particles;
>
> Tried to extract the combo coordinates from the combined micrographs.
>
> Error --- part of them extracted; part of them has wrong coordinates.
>
>
>
> And even with wrong coordinates if I run the 3d auto refinement I get the
> error Protocol failed: no path specified.
>
>
>
> b)    Combined all the micrographs in 1 project.
>
> Run MotionCor + CTF estimation
>
> Somehow import the combined coordinates from a) to this new project.
>
> Re-extract the coordinates.
>
>
>
>
>
> So I have a questions:
>
> -       Why a) doesn’t work? Is there a bug?
>
> -       How to export/import the combined coordinates into the new
> project?
>
> Amy other suggestions?
>
>
> p.s. when/if I succeed with a) with the particle polishing and ctf
> refinement work? The 2 datasets have different dose rate info.
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
>
>
>
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